Make HighFive patchable to allow PageBuffer in pHDF5. (#1784)

* brion: update highfive dependency.

* Enable applying pagebuffer patch to highfive.

bluebrain/repo-bluebrain/packages/brion/package.py

@@ -48,7 +48,8 @@ class Brion(CMakePackage):
  # TODO: bzip2 is a dependency of boost. Needed here because of linking
  # issue (libboost_iostreams.so.1.68.0 not finding libbz2.so)
  depends_on('bzip2')
- depends_on('[email protected] +boost', when='@3.3.8:')
+ depends_on('highfive +boost', when='@3.3.9:')
+ depends_on('[email protected] +boost', when='@3.3.8')
  depends_on('[email protected] +boost', when='@3.3.2:3.3.7')
  depends_on('[email protected] +boost', when='@:3.3.1')
  depends_on('mvdtool')

bluebrain/repo-bluebrain/packages/morpho-kit/package.py

@@ -31,8 +31,7 @@ class MorphoKit(CMakePackage):
  # The HighFive update is needed for paged HDF5 features. Unfortunately, the
  # page buffer is artificially unsupported in pHDF5. Hence, we depend on a
  # particular, patched version of HDF5.
- depends_on('[email protected]:', when='@0.3.5:')
- depends_on('[email protected]:+page_buffer_patch', when='@0.3.5:')
+ depends_on('[email protected]: +mpi+page_buffer_patch', when='@0.3.5:')
 
  # MPI is needed for the morphology merger.
  depends_on('mpi', when='@0.3.5:')

bluebrain/repo-patches/packages/highfive/package.py

@@ -41,17 +41,28 @@ class Highfive(CMakePackage):
  variant('mpi', default=True, description='Support MPI')
  variant('eigen', default=False, description='Support Eigen')
  variant('xtensor', default=False, description='Support xtensor')
+ variant('page_buffer_patch', default=False, when="@2.6.2",
+ description='Allow using the pagebuffer with pHDF5.')
 
  # Develop builds tests which require boost
  conflicts('~boost', when='@develop')
 
  depends_on('boost @1.41: +serialization+system', when='+boost')
  depends_on('hdf5 ~mpi', when='~mpi')
- depends_on('hdf5 +mpi', when='+mpi')
+ depends_on('hdf5 +mpi', when='+mpi~page_buffer_patch')
+
+ # Using the page buffer with pHDF5 requires HDF5 to be patched. This
+ # patch is currently only available for one version.
+ depends_on('[email protected] +page_buffer_patch+mpi', when='+mpi+page_buffer_patch')
+
  depends_on('eigen', when='+eigen')
  depends_on('xtensor', when='+xtensor')
  depends_on('mpi', when='+mpi')
 
+ # Enables the `PageBufferSize` property list also when building against pHDF5.
+ patch('remove-page-buffer-phdf5-check_v2.6.2.patch', when="+page_buffer_patch+mpi",
+ sha256="72a74f603bc957a9069c8e20abe28f303c4cab36d5d0e23bdcd6c6636fefe1f0")
+
  def cmake_args(self):
  return [
  '-DUSE_BOOST:Bool=' + str(self.spec.satisfies('+boost')),

bluebrain/repo-patches/packages/highfive/remove-page-buffer-phdf5-check_v2.6.2.patch

@@ -0,0 +1,47 @@
+diff --git i/deps/catch2 w/deps/catch2
+index 182c910..216713a 160000
+--- i/deps/catch2
++++ w/deps/catch2
+@@ -1 +1 @@
+-Subproject commit 182c910b4b63ff587a3440e08f84f70497e49a81
++Subproject commit 216713a4066b79d9803d374f261ccb30c0fb451f
+diff --git i/include/highfive/H5PropertyList.hpp w/include/highfive/H5PropertyList.hpp
+index 916e903..b3848f7 100644
+--- i/include/highfive/H5PropertyList.hpp
++++ w/include/highfive/H5PropertyList.hpp
+@@ -327,7 +327,6 @@ class FileSpacePageSize {
+ hsize_t _page_size;
+ };
+
+-#ifndef H5_HAVE_PARALLEL
+ /// \brief Set size of the page buffer.
+ ///
+ /// Please, consult the upstream documentation of
+@@ -360,7 +359,6 @@ class PageBufferSize {
+ unsigned _min_raw;
+ };
+ #endif
+-#endif
+
+ /// \brief Set hints as to how many links to expect and their average length
+ ///
+diff --git i/include/highfive/bits/H5PropertyList_misc.hpp w/include/highfive/bits/H5PropertyList_misc.hpp
+index a41707a..dcbba05 100644
+--- i/include/highfive/bits/H5PropertyList_misc.hpp
++++ w/include/highfive/bits/H5PropertyList_misc.hpp
+@@ -110,7 +110,6 @@ inline void FileSpacePageSize::apply(const hid_t list) const {
+ }
+ }
+
+-#ifndef H5_HAVE_PARALLEL
+ inline PageBufferSize::PageBufferSize(size_t page_buffer_size,
+ unsigned min_meta_percent,
+ unsigned min_raw_percent)
+@@ -124,7 +123,6 @@ inline void PageBufferSize::apply(const hid_t list) const {
+ }
+ }
+ #endif
+-#endif
+
+ #ifdef H5_HAVE_PARALLEL
+